From 695776f1d2b1c19fc0934842fbe8b7d880fdcec6 Mon Sep 17 00:00:00 2001 From: Chenxi Zhao Date: Fri, 28 Jul 2023 16:14:16 +0200 Subject: [PATCH 1/4] change getInterParticleDiffusionCoff() of Dirichlet wall boundary --- src/shared/materials/diffusion_reaction.h | 8 +- .../diffusion_dynamics.h | 18 ++--- .../diffusion_dynamics.hpp | 24 +++--- .../.idea/workspace.xml | 77 +++++++++++++++++++ 4 files changed, 102 insertions(+), 25 deletions(-) create mode 100644 tests/2d_examples/test_2d_dambreak_python/.idea/workspace.xml diff --git a/src/shared/materials/diffusion_reaction.h b/src/shared/materials/diffusion_reaction.h index 7fbc2ec1b0..29f7f22681 100644 --- a/src/shared/materials/diffusion_reaction.h +++ b/src/shared/materials/diffusion_reaction.h @@ -58,7 +58,7 @@ class BaseDiffusion : public BaseMaterial size_t gradient_species_index_; virtual Real getReferenceDiffusivity() = 0; - virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, Vecd &direction_from_j_to_i) = 0; + virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, const Vecd &direction_from_j_to_i) = 0; }; /** @@ -81,7 +81,7 @@ class IsotropicDiffusion : public BaseDiffusion virtual ~IsotropicDiffusion(){}; virtual Real getReferenceDiffusivity() override { return diff_cf_; }; - virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, Vecd &direction_from_j_to_i) override + virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, const Vecd &direction_from_j_to_i) override { return diff_cf_; }; @@ -118,7 +118,7 @@ class DirectionalDiffusion : public IsotropicDiffusion }; virtual Real getInterParticleDiffusionCoff(size_t particle_index_i, - size_t particle_index_j, Vecd &inter_particle_direction) override + size_t particle_index_j, const Vecd &inter_particle_direction) override { Vecd grad_ij = transformed_diffusivity_ * inter_particle_direction; return 1.0 / grad_ij.squaredNorm(); @@ -147,7 +147,7 @@ class LocalDirectionalDiffusion : public DirectionalDiffusion virtual void registerReloadLocalParameters(BaseParticles *base_particles) override; virtual void initializeLocalParameters(BaseParticles *base_particles) override; - virtual Real getInterParticleDiffusionCoff(size_t particle_index_i, size_t particle_index_j, Vecd &inter_particle_direction) override + virtual Real getInterParticleDiffusionCoff(size_t particle_index_i, size_t particle_index_j, const Vecd &inter_particle_direction) override { Matd trans_diffusivity = getAverageValue(local_transformed_diffusivity_[particle_index_i], local_transformed_diffusivity_[particle_index_j]); Vecd grad_ij = trans_diffusivity * inter_particle_direction; diff --git a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.h b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.h index 3d76f945de..fde593a07b 100644 --- a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.h +++ b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.h @@ -151,7 +151,7 @@ class CorrectedKernelGradientContact * @brief Base class for diffusion relaxation process between two contact bodies. */ template -class BaseDiffusionRelaxationContact +class BaseDiffusionRelaxationBoundary : public BaseDiffusionRelaxation, public DataDelegateContact { @@ -162,8 +162,8 @@ class BaseDiffusionRelaxationContact public: typedef BaseContactRelation BodyRelationType; - explicit BaseDiffusionRelaxationContact(BaseContactRelation &contact_relation); - virtual ~BaseDiffusionRelaxationContact(){}; + explicit BaseDiffusionRelaxationBoundary(BaseContactRelation &contact_relation); + virtual ~BaseDiffusionRelaxationBoundary(){}; }; /** @@ -172,11 +172,11 @@ class BaseDiffusionRelaxationContact */ template class DiffusionRelaxationDirichlet - : public BaseDiffusionRelaxationContact + : public BaseDiffusionRelaxationBoundary { protected: StdVec *>> contact_gradient_species_; - void getDiffusionChangeRateDirichletContact( + void getDiffusionChangeRateDirichlet( size_t particle_i, size_t particle_j, Vecd &e_ij, Real surface_area_ij, const StdVec *> &gradient_species_k); @@ -192,14 +192,14 @@ class DiffusionRelaxationDirichlet */ template class DiffusionRelaxationNeumann - : public BaseDiffusionRelaxationContact + : public BaseDiffusionRelaxationBoundary { StdLargeVec &n_; StdVec *> contact_heat_flux_; StdVec *> contact_n_; protected: - void getDiffusionChangeRateNeumannContact(size_t particle_i, size_t particle_j, + void getDiffusionChangeRateNeumann(size_t particle_i, size_t particle_j, Real surface_area_ij_Neumann, StdLargeVec &heat_flux_k); public: @@ -215,7 +215,7 @@ class DiffusionRelaxationNeumann */ template class DiffusionRelaxationRobin - : public BaseDiffusionRelaxationContact + : public BaseDiffusionRelaxationBoundary { StdLargeVec &n_; StdVec *> contact_convection_; @@ -223,7 +223,7 @@ class DiffusionRelaxationRobin StdVec *> contact_n_; protected: - void getDiffusionChangeRateRobinContact(size_t particle_i, size_t particle_j, Real surface_area_ij_Robin, StdLargeVec &convection_k, Real &T_infinity_k); + void getDiffusionChangeRateRobin(size_t particle_i, size_t particle_j, Real surface_area_ij_Robin, StdLargeVec &convection_k, Real &T_infinity_k); public: explicit DiffusionRelaxationRobin(BaseContactRelation &contact_relation); diff --git a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp index 1e016e65f0..3f329785ed 100644 --- a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp +++ b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp @@ -102,8 +102,8 @@ void DiffusionRelaxationInner:: } //=================================================================================================// template -BaseDiffusionRelaxationContact:: - BaseDiffusionRelaxationContact(BaseContactRelation &contact_relation) +BaseDiffusionRelaxationBoundary:: + BaseDiffusionRelaxationBoundary(BaseContactRelation &contact_relation) : BaseDiffusionRelaxation(contact_relation.getSPHBody()), DataDelegateContact(contact_relation) { @@ -140,7 +140,7 @@ BaseDiffusionRelaxationContact DiffusionRelaxationDirichlet:: DiffusionRelaxationDirichlet(BaseContactRelation &contact_relation) - : BaseDiffusionRelaxationContact(contact_relation) + : BaseDiffusionRelaxationBoundary(contact_relation) { contact_gradient_species_.resize(this->contact_particles_.size()); @@ -159,13 +159,13 @@ DiffusionRelaxationDirichlet void DiffusionRelaxationDirichlet:: - getDiffusionChangeRateDirichletContact(size_t particle_i, size_t particle_j, Vecd &e_ij, + getDiffusionChangeRateDirichlet(size_t particle_i, size_t particle_j, Vecd &e_ij, Real surface_area_ij, const StdVec *> &gradient_species_k) { for (size_t m = 0; m < this->all_diffusions_.size(); ++m) { Real diff_coff_ij = - this->all_diffusions_[m]->getInterParticleDiffusionCoff(particle_i, particle_j, e_ij); + this->all_diffusions_[m]->getInterParticleDiffusionCoff(particle_i, particle_i, Vecd::Zero()); Real phi_ij = (*this->gradient_species_[m])[particle_i] - (*gradient_species_k[m])[particle_j]; (*this->diffusion_dt_[m])[particle_i] += diff_coff_ij * phi_ij * surface_area_ij; } @@ -189,7 +189,7 @@ void DiffusionRelaxationDirichletcontact_kernel_gradients_[k](index_i, index_j, dW_ijV_j_, e_ij); Real area_ij = 2.0 * grad_ijV_j.dot(e_ij) / r_ij_; - getDiffusionChangeRateDirichletContact(index_i, index_j, e_ij, area_ij, gradient_species_k); + getDiffusionChangeRateDirichlet(index_i, index_j, e_ij, area_ij, gradient_species_k); } } } @@ -197,7 +197,7 @@ void DiffusionRelaxationDirichlet DiffusionRelaxationNeumann:: DiffusionRelaxationNeumann(BaseContactRelation &contact_relation) - : BaseDiffusionRelaxationContact(contact_relation), + : BaseDiffusionRelaxationBoundary(contact_relation), n_(this->particles_->n_) { contact_heat_flux_.resize(this->contact_particles_.size()); @@ -213,7 +213,7 @@ DiffusionRelaxationNeumann void DiffusionRelaxationNeumann:: - getDiffusionChangeRateNeumannContact(size_t particle_i, size_t particle_j, + getDiffusionChangeRateNeumann(size_t particle_i, size_t particle_j, Real surface_area_ij_Neumann, StdLargeVec &heat_flux_k) { for (size_t m = 0; m < this->all_diffusions_.size(); ++m) @@ -241,7 +241,7 @@ void DiffusionRelaxationNeumanncontact_kernel_gradients_[k](index_i, index_j, dW_ijV_j_, e_ij); Vecd n_ij = n_[index_i] - n_k[index_j]; Real area_ij_Neumann = grad_ijV_j.dot(n_ij); - getDiffusionChangeRateNeumannContact(index_i, index_j, area_ij_Neumann, heat_flux_k); + getDiffusionChangeRateNeumann(index_i, index_j, area_ij_Neumann, heat_flux_k); } } } @@ -249,7 +249,7 @@ void DiffusionRelaxationNeumann DiffusionRelaxationRobin:: DiffusionRelaxationRobin(BaseContactRelation &contact_relation) - : BaseDiffusionRelaxationContact(contact_relation), + : BaseDiffusionRelaxationBoundary(contact_relation), n_(this->particles_->n_) { contact_convection_.resize(this->contact_particles_.size()); @@ -268,7 +268,7 @@ DiffusionRelaxationRobin void DiffusionRelaxationRobin:: - getDiffusionChangeRateRobinContact(size_t particle_i, size_t particle_j, + getDiffusionChangeRateRobin(size_t particle_i, size_t particle_j, Real surface_area_ij_Robin, StdLargeVec &convection_k, Real &T_infinity_k) { for (size_t m = 0; m < this->all_diffusions_.size(); ++m) @@ -299,7 +299,7 @@ void DiffusionRelaxationRobincontact_kernel_gradients_[k](index_i, index_j, dW_ijV_j_, e_ij); Vecd n_ij = n_[index_i] - n_k[index_j]; Real area_ij_Robin = grad_ijV_j.dot(n_ij); - getDiffusionChangeRateRobinContact(index_i, index_j, area_ij_Robin, convection_k, T_infinity_k); + getDiffusionChangeRateRobin(index_i, index_j, area_ij_Robin, convection_k, T_infinity_k); } } } diff --git a/tests/2d_examples/test_2d_dambreak_python/.idea/workspace.xml b/tests/2d_examples/test_2d_dambreak_python/.idea/workspace.xml new file mode 100644 index 0000000000..9519898452 --- /dev/null +++ b/tests/2d_examples/test_2d_dambreak_python/.idea/workspace.xml @@ -0,0 +1,77 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1687264953679 + + + + \ No newline at end of file From 1e684df70e2a262445b45cd3104de40df8cbf723 Mon Sep 17 00:00:00 2001 From: Chenxi Zhao Date: Sat, 29 Jul 2023 18:36:21 +0200 Subject: [PATCH 2/4] change back to the name BaseDiffusionRelaxationContact --- .../diffusion_dynamics.h | 12 +-- .../diffusion_dynamics.hpp | 10 +-- .../.idea/workspace.xml | 77 ------------------- 3 files changed, 11 insertions(+), 88 deletions(-) delete mode 100644 tests/2d_examples/test_2d_dambreak_python/.idea/workspace.xml diff --git a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.h b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.h index fde593a07b..ab868f2dfe 100644 --- a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.h +++ b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.h @@ -151,7 +151,7 @@ class CorrectedKernelGradientContact * @brief Base class for diffusion relaxation process between two contact bodies. */ template -class BaseDiffusionRelaxationBoundary +class BaseDiffusionRelaxationContact : public BaseDiffusionRelaxation, public DataDelegateContact { @@ -162,8 +162,8 @@ class BaseDiffusionRelaxationBoundary public: typedef BaseContactRelation BodyRelationType; - explicit BaseDiffusionRelaxationBoundary(BaseContactRelation &contact_relation); - virtual ~BaseDiffusionRelaxationBoundary(){}; + explicit BaseDiffusionRelaxationContact(BaseContactRelation &contact_relation); + virtual ~BaseDiffusionRelaxationContact(){}; }; /** @@ -172,7 +172,7 @@ class BaseDiffusionRelaxationBoundary */ template class DiffusionRelaxationDirichlet - : public BaseDiffusionRelaxationBoundary + : public BaseDiffusionRelaxationContact { protected: StdVec *>> contact_gradient_species_; @@ -192,7 +192,7 @@ class DiffusionRelaxationDirichlet */ template class DiffusionRelaxationNeumann - : public BaseDiffusionRelaxationBoundary + : public BaseDiffusionRelaxationContact { StdLargeVec &n_; StdVec *> contact_heat_flux_; @@ -215,7 +215,7 @@ class DiffusionRelaxationNeumann */ template class DiffusionRelaxationRobin - : public BaseDiffusionRelaxationBoundary + : public BaseDiffusionRelaxationContact { StdLargeVec &n_; StdVec *> contact_convection_; diff --git a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp index 3f329785ed..6394816532 100644 --- a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp +++ b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp @@ -102,8 +102,8 @@ void DiffusionRelaxationInner:: } //=================================================================================================// template -BaseDiffusionRelaxationBoundary:: - BaseDiffusionRelaxationBoundary(BaseContactRelation &contact_relation) +BaseDiffusionRelaxationContact:: + BaseDiffusionRelaxationContact(BaseContactRelation &contact_relation) : BaseDiffusionRelaxation(contact_relation.getSPHBody()), DataDelegateContact(contact_relation) { @@ -140,7 +140,7 @@ BaseDiffusionRelaxationBoundary DiffusionRelaxationDirichlet:: DiffusionRelaxationDirichlet(BaseContactRelation &contact_relation) - : BaseDiffusionRelaxationBoundary(contact_relation) + : BaseDiffusionRelaxationContact(contact_relation) { contact_gradient_species_.resize(this->contact_particles_.size()); @@ -197,7 +197,7 @@ void DiffusionRelaxationDirichlet DiffusionRelaxationNeumann:: DiffusionRelaxationNeumann(BaseContactRelation &contact_relation) - : BaseDiffusionRelaxationBoundary(contact_relation), + : BaseDiffusionRelaxationContact(contact_relation), n_(this->particles_->n_) { contact_heat_flux_.resize(this->contact_particles_.size()); @@ -249,7 +249,7 @@ void DiffusionRelaxationNeumann DiffusionRelaxationRobin:: DiffusionRelaxationRobin(BaseContactRelation &contact_relation) - : BaseDiffusionRelaxationBoundary(contact_relation), + : BaseDiffusionRelaxationContact(contact_relation), n_(this->particles_->n_) { contact_convection_.resize(this->contact_particles_.size()); diff --git a/tests/2d_examples/test_2d_dambreak_python/.idea/workspace.xml b/tests/2d_examples/test_2d_dambreak_python/.idea/workspace.xml deleted file mode 100644 index 9519898452..0000000000 --- a/tests/2d_examples/test_2d_dambreak_python/.idea/workspace.xml +++ /dev/null @@ -1,77 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1687264953679 - - - - \ No newline at end of file From 013eedd91de279a1d5e66bcb177d4fc872c7a2b6 Mon Sep 17 00:00:00 2001 From: Chenxi Zhao Date: Sat, 29 Jul 2023 21:46:10 +0200 Subject: [PATCH 3/4] change back to eij --- src/shared/materials/diffusion_reaction.h | 8 ++++---- .../diffusion_reaction_dynamics/diffusion_dynamics.hpp | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/shared/materials/diffusion_reaction.h b/src/shared/materials/diffusion_reaction.h index 29f7f22681..7fbc2ec1b0 100644 --- a/src/shared/materials/diffusion_reaction.h +++ b/src/shared/materials/diffusion_reaction.h @@ -58,7 +58,7 @@ class BaseDiffusion : public BaseMaterial size_t gradient_species_index_; virtual Real getReferenceDiffusivity() = 0; - virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, const Vecd &direction_from_j_to_i) = 0; + virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, Vecd &direction_from_j_to_i) = 0; }; /** @@ -81,7 +81,7 @@ class IsotropicDiffusion : public BaseDiffusion virtual ~IsotropicDiffusion(){}; virtual Real getReferenceDiffusivity() override { return diff_cf_; }; - virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, const Vecd &direction_from_j_to_i) override + virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, Vecd &direction_from_j_to_i) override { return diff_cf_; }; @@ -118,7 +118,7 @@ class DirectionalDiffusion : public IsotropicDiffusion }; virtual Real getInterParticleDiffusionCoff(size_t particle_index_i, - size_t particle_index_j, const Vecd &inter_particle_direction) override + size_t particle_index_j, Vecd &inter_particle_direction) override { Vecd grad_ij = transformed_diffusivity_ * inter_particle_direction; return 1.0 / grad_ij.squaredNorm(); @@ -147,7 +147,7 @@ class LocalDirectionalDiffusion : public DirectionalDiffusion virtual void registerReloadLocalParameters(BaseParticles *base_particles) override; virtual void initializeLocalParameters(BaseParticles *base_particles) override; - virtual Real getInterParticleDiffusionCoff(size_t particle_index_i, size_t particle_index_j, const Vecd &inter_particle_direction) override + virtual Real getInterParticleDiffusionCoff(size_t particle_index_i, size_t particle_index_j, Vecd &inter_particle_direction) override { Matd trans_diffusivity = getAverageValue(local_transformed_diffusivity_[particle_index_i], local_transformed_diffusivity_[particle_index_j]); Vecd grad_ij = trans_diffusivity * inter_particle_direction; diff --git a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp index 6394816532..6ec7550ce5 100644 --- a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp +++ b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp @@ -165,7 +165,7 @@ void DiffusionRelaxationDirichletall_diffusions_.size(); ++m) { Real diff_coff_ij = - this->all_diffusions_[m]->getInterParticleDiffusionCoff(particle_i, particle_i, Vecd::Zero()); + this->all_diffusions_[m]->getInterParticleDiffusionCoff(particle_i, particle_i, e_ij); Real phi_ij = (*this->gradient_species_[m])[particle_i] - (*gradient_species_k[m])[particle_j]; (*this->diffusion_dt_[m])[particle_i] += diff_coff_ij * phi_ij * surface_area_ij; } From b3312e7ea1d545c69549bb47f7d9b91d75d37cd4 Mon Sep 17 00:00:00 2001 From: Chenxi Zhao Date: Tue, 1 Aug 2023 11:59:24 +0200 Subject: [PATCH 4/4] change all coff to coeff --- src/shared/materials/diffusion_reaction.h | 16 ++++++++-------- .../diffusion_dynamics.hpp | 12 ++++++------ .../test_0d_regression_test/regression_test.cpp | 6 +++--- .../test_2d_depolarization/depolarization.cpp | 6 +++--- .../2d_examples/test_2d_diffusion/diffusion.cpp | 6 +++--- .../diffusion_NeumannBC.h | 4 ++-- .../test_2d_heat_transfer/heat_transfer.cpp | 4 ++-- .../excitation-contraction.cpp | 8 ++++---- .../excitation_contraction.cpp | 2 +- .../excitation_contraction.h | 6 +++--- .../pkj_lv_electrocontraction.cpp | 4 ++-- .../pkj_lv_electrocontraction.h | 6 +++--- 12 files changed, 40 insertions(+), 40 deletions(-) diff --git a/src/shared/materials/diffusion_reaction.h b/src/shared/materials/diffusion_reaction.h index 7fbc2ec1b0..49c2e2c31a 100644 --- a/src/shared/materials/diffusion_reaction.h +++ b/src/shared/materials/diffusion_reaction.h @@ -58,7 +58,7 @@ class BaseDiffusion : public BaseMaterial size_t gradient_species_index_; virtual Real getReferenceDiffusivity() = 0; - virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, Vecd &direction_from_j_to_i) = 0; + virtual Real getInterParticleDiffusionCoeff(size_t particle_i, size_t particle_j, const Vecd &direction_from_j_to_i) = 0; }; /** @@ -81,7 +81,7 @@ class IsotropicDiffusion : public BaseDiffusion virtual ~IsotropicDiffusion(){}; virtual Real getReferenceDiffusivity() override { return diff_cf_; }; - virtual Real getInterParticleDiffusionCoff(size_t particle_i, size_t particle_j, Vecd &direction_from_j_to_i) override + virtual Real getInterParticleDiffusionCoeff(size_t particle_i, size_t particle_j, const Vecd &direction_from_j_to_i) override { return diff_cf_; }; @@ -117,8 +117,8 @@ class DirectionalDiffusion : public IsotropicDiffusion return SMAX(diff_cf_, diff_cf_ + bias_diff_cf_); }; - virtual Real getInterParticleDiffusionCoff(size_t particle_index_i, - size_t particle_index_j, Vecd &inter_particle_direction) override + virtual Real getInterParticleDiffusionCoeff(size_t particle_index_i, + size_t particle_index_j, const Vecd &inter_particle_direction) override { Vecd grad_ij = transformed_diffusivity_ * inter_particle_direction; return 1.0 / grad_ij.squaredNorm(); @@ -147,7 +147,7 @@ class LocalDirectionalDiffusion : public DirectionalDiffusion virtual void registerReloadLocalParameters(BaseParticles *base_particles) override; virtual void initializeLocalParameters(BaseParticles *base_particles) override; - virtual Real getInterParticleDiffusionCoff(size_t particle_index_i, size_t particle_index_j, Vecd &inter_particle_direction) override + virtual Real getInterParticleDiffusionCoeff(size_t particle_index_i, size_t particle_index_j, const Vecd &inter_particle_direction) override { Matd trans_diffusivity = getAverageValue(local_transformed_diffusivity_[particle_index_i], local_transformed_diffusivity_[particle_index_j]); Vecd grad_ij = trans_diffusivity * inter_particle_direction; @@ -293,10 +293,10 @@ class DiffusionReaction : public BaseMaterialType */ Real getDiffusionTimeStepSize(Real smoothing_length) { - Real diff_coff_max = 0.0; + Real diff_coeff_max = 0.0; for (size_t k = 0; k < all_diffusions_.size(); ++k) - diff_coff_max = SMAX(diff_coff_max, all_diffusions_[k]->getReferenceDiffusivity()); - return 0.5 * smoothing_length * smoothing_length / diff_coff_max / Real(Dimensions); + diff_coeff_max = SMAX(diff_coeff_max, all_diffusions_[k]->getReferenceDiffusivity()); + return 0.5 * smoothing_length * smoothing_length / diff_coeff_max / Real(Dimensions); }; /** Initialize a diffusion material. */ diff --git a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp index 6ec7550ce5..966f603064 100644 --- a/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp +++ b/src/shared/particle_dynamics/diffusion_reaction_dynamics/diffusion_dynamics.hpp @@ -75,11 +75,11 @@ void DiffusionRelaxationInner:: { for (size_t m = 0; m < this->all_diffusions_.size(); ++m) { - Real diff_coff_ij = - this->all_diffusions_[m]->getInterParticleDiffusionCoff(particle_i, particle_j, e_ij); + Real diff_coeff_ij = + this->all_diffusions_[m]->getInterParticleDiffusionCoeff(particle_i, particle_j, e_ij); StdLargeVec &gradient_species = *this->gradient_species_[m]; Real phi_ij = gradient_species[particle_i] - gradient_species[particle_j]; - (*this->diffusion_dt_[m])[particle_i] += diff_coff_ij * phi_ij * surface_area_ij; + (*this->diffusion_dt_[m])[particle_i] += diff_coeff_ij * phi_ij * surface_area_ij; } } //=================================================================================================// @@ -164,10 +164,10 @@ void DiffusionRelaxationDirichletall_diffusions_.size(); ++m) { - Real diff_coff_ij = - this->all_diffusions_[m]->getInterParticleDiffusionCoff(particle_i, particle_i, e_ij); + Real diff_coeff_ij = + this->all_diffusions_[m]->getInterParticleDiffusionCoeff(particle_i, particle_i, e_ij); Real phi_ij = (*this->gradient_species_[m])[particle_i] - (*gradient_species_k[m])[particle_j]; - (*this->diffusion_dt_[m])[particle_i] += diff_coff_ij * phi_ij * surface_area_ij; + (*this->diffusion_dt_[m])[particle_i] += diff_coeff_ij * phi_ij * surface_area_ij; } } //=================================================================================================// diff --git a/tests/2d_examples/test_0d_regression_test/regression_test.cpp b/tests/2d_examples/test_0d_regression_test/regression_test.cpp index f039446ebe..95f7ed158c 100644 --- a/tests/2d_examples/test_0d_regression_test/regression_test.cpp +++ b/tests/2d_examples/test_0d_regression_test/regression_test.cpp @@ -19,8 +19,8 @@ BoundingBox system_domain_bounds(Vec2d(-BW, -BW), Vec2d(L + BW, H + BW)); //---------------------------------------------------------------------- // Global parameters on material properties //---------------------------------------------------------------------- -Real diffusion_coff = 1.0e-3; -Real bias_coff = 0.0; +Real diffusion_coeff = 1.0e-3; +Real bias_coeff = 0.0; Real alpha = Pi / 4.0; Vec2d bias_direction(cos(alpha), sin(alpha)); Real initial_temperature = 0.0; @@ -103,7 +103,7 @@ class DiffusionMaterial : public DiffusionReaction public: DiffusionMaterial() : DiffusionReaction({"Phi"}, SharedPtr()) { - initializeAnDiffusion("Phi", "Phi", diffusion_coff, bias_coff, bias_direction); + initializeAnDiffusion("Phi", "Phi", diffusion_coeff, bias_coeff, bias_direction); }; }; //---------------------------------------------------------------------- diff --git a/tests/2d_examples/test_2d_depolarization/depolarization.cpp b/tests/2d_examples/test_2d_depolarization/depolarization.cpp index 042c8c5d62..8bbc294d1d 100644 --- a/tests/2d_examples/test_2d_depolarization/depolarization.cpp +++ b/tests/2d_examples/test_2d_depolarization/depolarization.cpp @@ -18,8 +18,8 @@ StdVec observation_location = {Vecd(0.3, 0.7)}; //---------------------------------------------------------------------- // Basic parameters for material properties. //---------------------------------------------------------------------- -Real diffusion_coff = 1.0; -Real bias_coff = 0.0; +Real diffusion_coeff = 1.0; +Real bias_coeff = 0.0; Vec2d fiber_direction(1.0, 0.0); Real c_m = 1.0; Real k = 8.0; @@ -83,7 +83,7 @@ int main() SolidBody muscle_body(system, makeShared("MuscleBlock")); SharedPtr muscle_reaction_model_ptr = makeShared(k_a, c_m, k, a, b, mu_1, mu_2, epsilon); muscle_body.defineParticlesAndMaterial( - muscle_reaction_model_ptr, TypeIdentity(), diffusion_coff, bias_coff, fiber_direction); + muscle_reaction_model_ptr, TypeIdentity(), diffusion_coeff, bias_coeff, fiber_direction); muscle_body.generateParticles(); ObserverBody voltage_observer(system, "VoltageObserver"); diff --git a/tests/2d_examples/test_2d_diffusion/diffusion.cpp b/tests/2d_examples/test_2d_diffusion/diffusion.cpp index 3038393660..cbf545e18e 100644 --- a/tests/2d_examples/test_2d_diffusion/diffusion.cpp +++ b/tests/2d_examples/test_2d_diffusion/diffusion.cpp @@ -15,8 +15,8 @@ BoundingBox system_domain_bounds(Vec2d(0.0, 0.0), Vec2d(L, H)); //---------------------------------------------------------------------- // Basic parameters for material properties. //---------------------------------------------------------------------- -Real diffusion_coff = 1.0e-4; -Real bias_coff = 0.0; +Real diffusion_coeff = 1.0e-4; +Real bias_coeff = 0.0; Real alpha = Pi / 6.0; Vec2d bias_direction(cos(alpha), sin(alpha)); //---------------------------------------------------------------------- @@ -44,7 +44,7 @@ class DiffusionMaterial : public DiffusionReaction public: DiffusionMaterial() : DiffusionReaction({"Phi"}, SharedPtr()) { - initializeAnDiffusion("Phi", "Phi", diffusion_coff, bias_coff, bias_direction); + initializeAnDiffusion("Phi", "Phi", diffusion_coeff, bias_coeff, bias_direction); }; }; using DiffusionParticles = DiffusionReactionParticles; diff --git a/tests/2d_examples/test_2d_diffusion_NeumannBC/diffusion_NeumannBC.h b/tests/2d_examples/test_2d_diffusion_NeumannBC/diffusion_NeumannBC.h index 6c73c8c6bf..bf3d1da777 100644 --- a/tests/2d_examples/test_2d_diffusion_NeumannBC/diffusion_NeumannBC.h +++ b/tests/2d_examples/test_2d_diffusion_NeumannBC/diffusion_NeumannBC.h @@ -20,7 +20,7 @@ BoundingBox system_domain_bounds(Vec2d(-BW, -BW), Vec2d(L + BW, H + BW)); //---------------------------------------------------------------------- // Basic parameters for material properties. //---------------------------------------------------------------------- -Real diffusion_coff = 1; +Real diffusion_coeff = 1; std::array species_name_list{"Phi"}; //---------------------------------------------------------------------- // Initial and boundary conditions. @@ -95,7 +95,7 @@ class DiffusionMaterial : public DiffusionReaction public: DiffusionMaterial() : DiffusionReaction({"Phi"}, SharedPtr()) { - initializeAnDiffusion("Phi", "Phi", diffusion_coff); + initializeAnDiffusion("Phi", "Phi", diffusion_coeff); } }; using DiffusionParticles = DiffusionReactionParticles; diff --git a/tests/2d_examples/test_2d_heat_transfer/heat_transfer.cpp b/tests/2d_examples/test_2d_heat_transfer/heat_transfer.cpp index cd46f8e423..9272abf570 100644 --- a/tests/2d_examples/test_2d_heat_transfer/heat_transfer.cpp +++ b/tests/2d_examples/test_2d_heat_transfer/heat_transfer.cpp @@ -20,7 +20,7 @@ StdVec observation_location = {Vecd(0.0, DH * 0.5)}; //---------------------------------------------------------------------- // Global parameters on the material properties //---------------------------------------------------------------------- -Real diffusion_coff = 1.0e-3; +Real diffusion_coeff = 1.0e-3; Real rho0_f = 1.0; /**< Density. */ Real U_f = 1.0; /**< Characteristic velocity. */ Real c_f = 10.0 * U_f; /**< Speed of sound. */ @@ -101,7 +101,7 @@ class ThermofluidBodyMaterial : public DiffusionReaction({"Phi"}, SharedPtr(), rho0_f, c_f, mu_f) { - initializeAnDiffusion("Phi", "Phi", diffusion_coff); + initializeAnDiffusion("Phi", "Phi", diffusion_coeff); }; }; using DiffusionBaseParticles = DiffusionReactionParticles; diff --git a/tests/3d_examples/test_3d_heart_electromechanics/excitation-contraction.cpp b/tests/3d_examples/test_3d_heart_electromechanics/excitation-contraction.cpp index b7c646d972..d9a7b1ace9 100644 --- a/tests/3d_examples/test_3d_heart_electromechanics/excitation-contraction.cpp +++ b/tests/3d_examples/test_3d_heart_electromechanics/excitation-contraction.cpp @@ -36,8 +36,8 @@ Real poisson = 0.4995; Real bulk_modulus = 2.0 * a0[0] * (1.0 + poisson) / (3.0 * (1.0 - 2.0 * poisson)); /** Electrophysiology parameters. */ std::array species_name_list{"Phi"}; -Real diffusion_coff = 0.8; -Real bias_coff = 0.0; +Real diffusion_coeff = 0.8; +Real bias_coeff = 0.0; /** Electrophysiology parameters. */ Real c_m = 1.0; Real k = 8.0; @@ -72,7 +72,7 @@ class FiberDirectionDiffusion : public DiffusionReaction(), rho0_s, bulk_modulus, fiber_direction, sheet_direction, a0, b0) { - initializeAnDiffusion("Phi", "Phi", diffusion_coff); + initializeAnDiffusion("Phi", "Phi", diffusion_coeff); }; }; using FiberDirectionDiffusionParticles = DiffusionReactionParticles; @@ -363,7 +363,7 @@ int main(int ac, char *av[]) SharedPtr muscle_reaction_model_ptr = makeShared(k_a, c_m, k, a, b, mu_1, mu_2, epsilon); physiology_heart.defineParticlesAndMaterial< ElectroPhysiologyParticles, MonoFieldElectroPhysiology>( - muscle_reaction_model_ptr, TypeIdentity(), diffusion_coff, bias_coff, fiber_direction); + muscle_reaction_model_ptr, TypeIdentity(), diffusion_coeff, bias_coeff, fiber_direction); (!system.RunParticleRelaxation() && system.ReloadParticles()) ? physiology_heart.generateParticles(io_environment, "HeartModel") : physiology_heart.generateParticles(); diff --git a/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.cpp b/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.cpp index b963bf866c..e43d1db99e 100644 --- a/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.cpp +++ b/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.cpp @@ -114,7 +114,7 @@ int main(int ac, char *av[]) SharedPtr muscle_reaction_model_ptr = makeShared(k_a, c_m, k, a, b, mu_1, mu_2, epsilon); physiology_heart.defineParticlesAndMaterial< ElectroPhysiologyParticles, MonoFieldElectroPhysiology>( - muscle_reaction_model_ptr, TypeIdentity(), diffusion_coff, bias_coff, fiber_direction); + muscle_reaction_model_ptr, TypeIdentity(), diffusion_coeff, bias_coeff, fiber_direction); (!system.RunParticleRelaxation() && system.ReloadParticles()) ? physiology_heart.generateParticles(io_environment, "HeartModel") : physiology_heart.generateParticles(); diff --git a/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.h b/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.h index 139d15f79e..7698b72971 100644 --- a/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.h +++ b/tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.h @@ -39,8 +39,8 @@ Real poisson = 0.4995; Real bulk_modulus = 2.0 * a0[0] * (1.0 + poisson) / (3.0 * (1.0 - 2.0 * poisson)); /** Electrophysiology parameters. */ std::array species_name_list{"Phi"}; -Real diffusion_coff = 0.8; -Real bias_coff = 0.0; +Real diffusion_coeff = 0.8; +Real bias_coeff = 0.0; /** Electrophysiology parameters. */ Real c_m = 1.0; Real k = 8.0; @@ -74,7 +74,7 @@ class FiberDirectionDiffusion : public DiffusionReaction(), rho0_s, bulk_modulus, fiber_direction, sheet_direction, a0, b0) { - initializeAnDiffusion("Phi", "Phi", diffusion_coff); + initializeAnDiffusion("Phi", "Phi", diffusion_coeff); }; }; using FiberDirectionDiffusionParticles = DiffusionReactionParticles; diff --git a/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.cpp b/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.cpp index 34e297d292..f2f7a07798 100644 --- a/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.cpp +++ b/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.cpp @@ -129,7 +129,7 @@ int main(int ac, char *av[]) SharedPtr muscle_reaction_model_ptr = makeShared(k_a, c_m, k, a, b, mu_1, mu_2, epsilon); physiology_heart.defineParticlesAndMaterial< ElectroPhysiologyParticles, MonoFieldElectroPhysiology>( - muscle_reaction_model_ptr, TypeIdentity(), diffusion_coff, bias_coff, fiber_direction); + muscle_reaction_model_ptr, TypeIdentity(), diffusion_coeff, bias_coeff, fiber_direction); (!system.RunParticleRelaxation() && system.ReloadParticles()) ? physiology_heart.generateParticles(io_environment, "HeartModel") : physiology_heart.generateParticles(); @@ -147,7 +147,7 @@ int main(int ac, char *av[]) SharedPtr pkj_reaction_model_ptr = makeShared(k_a, c_m, k, a, b, mu_1, mu_2, epsilon); pkj_body.defineParticlesAndMaterial< ElectroPhysiologyReducedParticles, MonoFieldElectroPhysiology>( - pkj_reaction_model_ptr, TypeIdentity(), diffusion_coff * acceleration_factor, bias_coff, fiber_direction); + pkj_reaction_model_ptr, TypeIdentity(), diffusion_coeff * acceleration_factor, bias_coeff, fiber_direction); pkj_body.generateParticles(starting_point, second_point, 50, 1.0); TreeTerminates pkj_leaves(pkj_body); //---------------------------------------------------------------------- diff --git a/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.h b/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.h index 57596cfd51..a19e35dd90 100644 --- a/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.h +++ b/tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.h @@ -64,8 +64,8 @@ Real poisson = 0.4995; Real bulk_modulus = 2.0 * a0[0] * (1.0 + poisson) / (3.0 * (1.0 - 2.0 * poisson)); /** Electrophysiology parameters. */ Real acceleration_factor = 27.5; /** Acceleration factor for fast diffusion on purkinje network. */ -Real diffusion_coff = 0.8; -Real bias_coff = 0.0; +Real diffusion_coeff = 0.8; +Real bias_coeff = 0.0; /** Electrophysiology parameters. */ std::array species_name_list{"Phi"}; Real c_m = 1.0; @@ -104,7 +104,7 @@ class FiberDirectionDiffusion : public DiffusionReaction(), rho0_s, bulk_modulus, fiber_direction, sheet_direction, a0, b0) { - initializeAnDiffusion("Phi", "Phi", diffusion_coff); + initializeAnDiffusion("Phi", "Phi", diffusion_coeff); }; }; using FiberDirectionDiffusionParticles = DiffusionReactionParticles;